How about an increase to the regular AI progress as long as the player is allied to Sphere? It would make sense from an in-game perspective. I'd think the AIs would certainly find an alliance between the remaining humans and a Megastructure of awesome power like the Sphere alarming. As the AI progress goes up, this would increase difficulty in a natural manner, while avoiding any potentially messy rebalancing of the Dyson Gatlings or the like. So now players have a choice, a powerful ally with massive defensive potential for sure, but at the risk of bringing the AI wrath-hammer down that much faster, that much more often and creating tougher situations overall.
Furthermore, this could receive the same treatment as Golems did and the Spirecraft. For those who want the Sphere to remain as it is in-game, you could have an Easy Dyson Sphere option. Medium Dyson Sphere would include the AI regular increase to AI progress every half hour. For the hard option either more AI progress increase or keep it the same and something fun, like an Exogalactic Strikeforce to make those Gatlings really earn their keep.